double calculateCosY(const RDGeom::Point3D &iPoint,
const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint,
const RDGeom::Point3D &lPoint) {
RDGeom::Point3D rJI = iPoint - jPoint;
RDGeom::Point3D rJK = kPoint - jPoint;
RDGeom::Point3D rJL = lPoint - jPoint;
rJI /= rJI.length();
rJK /= rJK.length();
rJL /= rJL.length();
RDGeom::Point3D n = rJI.crossProduct(rJK);
n /= n.length();
return n.dotProduct(rJL);
}
void testIssue216() {
RDNumeric::DoubleSymmMatrix dmat(4);
dmat.setVal(0, 0, 0.0);
dmat.setVal(0, 1, 1.0);
dmat.setVal(0, 2, 1.0);
dmat.setVal(0, 3, 1.0);
dmat.setVal(1, 1, 0.0);
dmat.setVal(1, 2, 1.0);
dmat.setVal(1, 3, 1.0);
dmat.setVal(2, 2, 0.0);
dmat.setVal(2, 3, 1.0);
dmat.setVal(3, 3, 0.0);
std::cout << dmat;
RDGeom::PointPtrVect pos;
for (int i = 0; i < 4; i++) {
RDGeom::Point3D *pt = new RDGeom::Point3D();
pos.push_back(pt);
}
bool gotCoords = DistGeom::computeInitialCoords(dmat, pos);
CHECK_INVARIANT(gotCoords, "");
for (int i = 1; i < 4; i++) {
RDGeom::Point3D pti = *(RDGeom::Point3D *)pos[i];
for (int j = 0; j < i; j++) {
RDGeom::Point3D ptj = *(RDGeom::Point3D *)pos[j];
ptj -= pti;
CHECK_INVARIANT(RDKit::feq(ptj.length(), 1.0, 0.02), "");
}
}
}
double calcOopChi(const RDGeom::Point3D &iPoint, const RDGeom::Point3D &jPoint,
const RDGeom::Point3D &kPoint,
const RDGeom::Point3D &lPoint) {
RDGeom::Point3D rJI = iPoint - jPoint;
RDGeom::Point3D rJK = kPoint - jPoint;
RDGeom::Point3D rJL = lPoint - jPoint;
rJI /= rJI.length();
rJK /= rJK.length();
rJL /= rJL.length();
RDGeom::Point3D n = rJI.crossProduct(rJK);
n /= n.length();
double sinChi = n.dotProduct(rJL);
clipToOne(sinChi);
return RAD2DEG * asin(sinChi);
}
void setBondLength(Conformer &conf,
unsigned int iAtomId, unsigned int jAtomId, double value) {
RDGeom::POINT3D_VECT &pos = conf.getPositions();
RANGE_CHECK(0, iAtomId, pos.size() - 1);
RANGE_CHECK(0, jAtomId, pos.size() - 1);
ROMol &mol = conf.getOwningMol();
Bond *bond = mol.getBondBetweenAtoms(iAtomId, jAtomId);
if(!bond) throw ValueErrorException("atoms i and j must be bonded");
if(queryIsBondInRing(bond)) throw ValueErrorException("bond (i,j) must not belong to a ring");
RDGeom::Point3D v = pos[iAtomId] - pos[jAtomId];
double origValue = v.length();
if(origValue <= 1.e-8) throw ValueErrorException("atoms i and j have identical 3D coordinates");
// get all atoms bonded to j
std::list<unsigned int> alist;
_toBeMovedIdxList(mol, iAtomId, jAtomId, alist);
v *= (value / origValue - 1.);
for (std::list<unsigned int>::iterator it = alist.begin(); it != alist.end(); ++it) {
pos[*it] -= v;
}
}
void InversionContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D p1(pos[3 * d_at1Idx],
pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D p2(pos[3 * d_at2Idx],
pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D p3(pos[3 * d_at3Idx],
pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D p4(pos[3 * d_at4Idx],
pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g1 = &(grad[3 * d_at1Idx]);
double *g2 = &(grad[3 * d_at2Idx]);
double *g3 = &(grad[3 * d_at3Idx]);
double *g4 = &(grad[3 * d_at4Idx]);
RDGeom::Point3D rJI = p1 - p2;
RDGeom::Point3D rJK = p3 - p2;
RDGeom::Point3D rJL = p4 - p2;
double dJI = rJI.length();
double dJK = rJK.length();
double dJL = rJL.length();
if (isDoubleZero(dJI) || isDoubleZero(dJK) || isDoubleZero(dJL)) {
return;
}
rJI /= dJI;
rJK /= dJK;
rJL /= dJL;
RDGeom::Point3D n = (-rJI).crossProduct(rJK);
n /= n.length();
double cosY = n.dotProduct(rJL);
double sinYSq = 1.0 - cosY * cosY;
double sinY = std::max(((sinYSq > 0.0) ? sqrt(sinYSq) : 0.0), 1.0e-8);
double cosTheta = rJI.dotProduct(rJK);
double sinThetaSq = std::max(1.0 - cosTheta * cosTheta, 1.0e-8);
double sinTheta = std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
// sin(2 * W) = 2 * sin(W) * cos(W) = 2 * cos(Y) * sin(Y)
double dE_dW = -d_forceConstant
* (d_C1 * cosY - 4.0 * d_C2 * cosY * sinY);
RDGeom::Point3D t1 = rJL.crossProduct(rJK);
RDGeom::Point3D t2 = rJI.crossProduct(rJL);
RDGeom::Point3D t3 = rJK.crossProduct(rJI);
double term1 = sinY * sinTheta;
double term2 = cosY / (sinY * sinThetaSq);
double tg1[3] = { (t1.x / term1 - (rJI.x - rJK.x * cosTheta) * term2) / dJI,
(t1.y / term1 - (rJI.y - rJK.y * cosTheta) * term2) / dJI,
(t1.z / term1 - (rJI.z - rJK.z * cosTheta) * term2) / dJI };
double tg3[3] = { (t2.x / term1 - (rJK.x - rJI.x * cosTheta) * term2) / dJK,
(t2.y / term1 - (rJK.y - rJI.y * cosTheta) * term2) / dJK,
(t2.z / term1 - (rJK.z - rJI.z * cosTheta) * term2) / dJK };
double tg4[3] = { (t3.x / term1 - rJL.x * cosY / sinY) / dJL,
(t3.y / term1 - rJL.y * cosY / sinY) / dJL,
(t3.z / term1 - rJL.z * cosY / sinY) / dJL };
for (unsigned int i = 0; i < 3; ++i) {
g1[i] += dE_dW * tg1[i];
g2[i] += -dE_dW * (tg1[i] + tg3[i] + tg4[i]);
g3[i] += dE_dW * tg3[i];
g4[i] += dE_dW * tg4[i];
}
}
void OopBendContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D iPoint(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g1 = &(grad[3 * d_at1Idx]);
double *g2 = &(grad[3 * d_at2Idx]);
double *g3 = &(grad[3 * d_at3Idx]);
double *g4 = &(grad[3 * d_at4Idx]);
RDGeom::Point3D rJI = iPoint - jPoint;
RDGeom::Point3D rJK = kPoint - jPoint;
RDGeom::Point3D rJL = lPoint - jPoint;
double dJI = rJI.length();
double dJK = rJK.length();
double dJL = rJL.length();
if (isDoubleZero(dJI) || isDoubleZero(dJK) || isDoubleZero(dJL)) {
return;
}
rJI /= dJI;
rJK /= dJK;
rJL /= dJL;
RDGeom::Point3D n = (-rJI).crossProduct(rJK);
n /= n.length();
double const c2 = MDYNE_A_TO_KCAL_MOL * DEG2RAD * DEG2RAD;
double sinChi = rJL.dotProduct(n);
clipToOne(sinChi);
double cosChiSq = 1.0 - sinChi * sinChi;
double cosChi = std::max(((cosChiSq > 0.0) ? sqrt(cosChiSq) : 0.0), 1.0e-8);
double chi = RAD2DEG * asin(sinChi);
double cosTheta = rJI.dotProduct(rJK);
clipToOne(cosTheta);
double sinThetaSq = std::max(1.0 - cosTheta * cosTheta, 1.0e-8);
double sinTheta =
std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
double dE_dChi = RAD2DEG * c2 * d_koop * chi;
RDGeom::Point3D t1 = rJL.crossProduct(rJK);
RDGeom::Point3D t2 = rJI.crossProduct(rJL);
RDGeom::Point3D t3 = rJK.crossProduct(rJI);
double term1 = cosChi * sinTheta;
double term2 = sinChi / (cosChi * sinThetaSq);
double tg1[3] = {(t1.x / term1 - (rJI.x - rJK.x * cosTheta) * term2) / dJI,
(t1.y / term1 - (rJI.y - rJK.y * cosTheta) * term2) / dJI,
(t1.z / term1 - (rJI.z - rJK.z * cosTheta) * term2) / dJI};
double tg3[3] = {(t2.x / term1 - (rJK.x - rJI.x * cosTheta) * term2) / dJK,
(t2.y / term1 - (rJK.y - rJI.y * cosTheta) * term2) / dJK,
(t2.z / term1 - (rJK.z - rJI.z * cosTheta) * term2) / dJK};
double tg4[3] = {(t3.x / term1 - rJL.x * sinChi / cosChi) / dJL,
(t3.y / term1 - rJL.y * sinChi / cosChi) / dJL,
(t3.z / term1 - rJL.z * sinChi / cosChi) / dJL};
for (unsigned int i = 0; i < 3; ++i) {
g1[i] += dE_dChi * tg1[i];
g2[i] += -dE_dChi * (tg1[i] + tg3[i] + tg4[i]);
g3[i] += dE_dChi * tg3[i];
g4[i] += dE_dChi * tg4[i];
}
}
bool comparePts(const RDGeom::Point3D &pt1, const RDGeom::Point3D &pt2, double tol=1.0e-4) {
RDGeom::Point3D tpt = pt1;
tpt -= pt2;
return (tpt.length() < tol);
}